A jalapeño pepper grown in Mexico and stored in a Texas border town warehouse has tested positive for the same rare strain of salmonella that has confounded federal disease investigators for nearly two months.

The test on the hot pepper was the first to find the germ on any type of produce item since state and federal health authorities first warned of the stomach bug on June 3. As a result, the Food and Drug Administration issued an advisory Monday for consumers to avoid eating uncooked jalapeños from any source - another potential blow to California, which produces about $45 million worth of chile peppers annually.

Early on, the agency linked the salmonella strain to fresh tomatoes, taking a 40 percent bite out of California fresh tomato sales this summer despite the fact that the state's crop has never been implicated in the outbreak.

Although the FDA still believes that fresh tomatoes may have been a source of the bacteria in the early days of the outbreak, last week it said it is now safe to eat them because the trail had now turned toward fresh peppers.

Dr. David Acheson, the beleaguered FDA associate commissioner in charge of the probe, on Monday called the discovery of a genetic match for the salmonella strain on the jalapeño "a very important break in the case," although the ultimate source of the contamination has yet to be found.

Acheson was clear that, although the pepper came from a farm in Mexico, it has yet to be determined whether the source of contamination was on the farm, at the distributor or somewhere in between.

The latest news provides little solace to tomato growers. "It's a great relief to know it's not tomatoes, even though the CDC (federal Centers for Disease Control and Prevention) and the FDA will never admit it wasn't tomatoes," said Tom Nassif, chief executive of Western Growers, the Irvine farm group representing producers of about half the produce grown in the United States.

Nassif said he believes the outbreak was caused by one farm in Mexico, or one distribution center, but the advisory put out by the government implicates an entire industry.

"Everybody across the country is going to suffer enormous damages," he said.

Acheson maintains that, during the initial outbreak - where cases were found as early as April 10 - there was a "clear association" with consumption of fresh tomatoes. Only later were peppers clearly implicated, as well.

"Tomatoes are not exonerated as the cause of this outbreak," he said. However, because all the latest cases have been linked to peppers, the FDA said it is now safe to eat fresh tomatoes from anywhere.

The tainted pepper was picked up last week by disease detectives tracing back the source of peppers believed to have sickened a group of Texas restaurant patrons. Since April, the CDC has logged 1,251 cases of the Saintpaul strain of salmonella in 43 states.

Only nine cases have been reported in California. There have been 475 in Texas.

The pepper was found at Agricola Zaragoza, a produce distributor in McAllen, Texas, a small town just a few miles from the Rio Grande at the southernmost tip of the state. The company has voluntarily recalled an undisclosed amount of fresh jalapeños distributed since June 30.

The FDA characterized Agricola Zaragoza as "a relatively small company" that may sort products from the farm before shipping them to customers. Besides peppers, the McAllen site also handles tomatillos, a small tomato that comes in a papery husk and, like jalapeños, is often an ingredient in salsa.

FDA and CDC investigators are continuing to try to find the source of the outbreak. They are on site in Mexico looking at farms and are studying the distribution center to see if the peppers could have been tainted during the handling and sorting process.

Although there have been no reports of illness since July 4, there still may be contaminated peppers in the marketplace. "This outbreak continues," said Dr. Robert Tauxe, deputy director for food-borne illnesses at the CDC. "We do not believe it has ended at this point."

Consumers are cautioned to avoid products like fresh salsa that may contain chile peppers of unknown provenance. The FDA is also cautioning consumers who are at increased risk of severe infection, including infants, the elderly and those with impaired immune systems not to eat serrano peppers, which are hard to distinguish from jalapeños.

Cooked or pickled peppers found in jars are deemed safe to eat, as are processed rather than fresh salsas.

New Mexico is the largest U.S. producer of fresh chile peppers, but the harvest season there has yet to begin. UC Davis researcher Trevor Suslow said that California accounts for about $45 million, or 15 percent, of U.S. sales of fresh chile peppers. They are grown in the irrigated desert of the Imperial County and as far north as Monterey and Santa Clara counties.